Implement New Technologies in NBS: Next Generation Sequencing in NBS for Cystic Fibrosis

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1 Implement New Technologies in NBS: Next Generation Sequencing in NBS for Cystic Fibrosis Mei Baker, MD, FACMG Co-Director, Newborn Laboratory at WSLH Professor, Department of Pediatrics University of Wisconsin School of Medicine and Public health Gene Sequencing in Public Health Newborn Meeting Atlanta, GA February 16-17, 2017 Robert Guthrie, MD, PhD ( ) Advances in technology and methodology have often driven improved screening procedures!!! 1

2 Progression of CF NBS Tests IRT IRT/DNA IRT/DNA* IRT/DNA/DNA** (F508del) (CFTR-23) (CFTR > 200) *With IRT/DNA, 10 heterozygote carriers are detected for every CF infant diagnosed. **IRT/NGS algorithm applying CFTR2 knowledge and next generation sequencing capability, which may be a game-changer. CFTR2 Mutation List History Number of Patients V1 4/10/2012 V2 7/22/2013 V3 2/27/2015 V4 8/13/2015 V5 8/8/ ,312 39,696 39,696 88,664 88,664 CF causing Varying Clinical Consequence Non CFcausing Unknown Significance Total

3 IRT/NGS in NBS for CF IRT NGS CFTR mutations panel Normal?? One Mut. Two Mut. Positive Technical Feasibility Study 3

4 NGS CF Assay A validated assay using newborn screening dried blood specimens Cover all CFTR exons and known intronic CF causing mutations Include Ex2-3 and Ex22-23 deletion Simultaneously detect all mutations in a predetermined panel Prospective Study SPECIFIC AIM 1. We will further modify the established Illumina NGS method to expand CFTR mutation panel up to 250 CF-causing mutations. SPECIFIC AIM 2. We will demonstrate that the IRT/NGS CF screening protocol can significantly reduce false positive results caused by identification of CF heterozygote carrier infants in a real-world NBS environment. 4

5 Flowchart (Incorporating NGS) ACMG 23 Mutation Panel IRT (top 4%, daily) Next Gen Sequencing Expanded Panel No One Mutation Two Two One Mutation No PRELIMINARY REPORT Abnormal Report / Call to Physician FINAL REPORT Results Reported; note indicating NGS result to follow Results Reported and sweat test requested; note indicating NGS result to follow Results to PCP and sweat test requested; call to physician Results Reported Flowchart (NGS only since April 1, 2016) PRELIMINARY REPORT IRT (top 4%, daily) Next Gen Sequencing Two One Mutation FINAL REPORT Results to PCP and sweat test requested; call to physician No Normal Report 5

6 Updated IRT/NGS in NBS for CF IRT NGS CFTR Panel (CF Causing ) Positive Two Mut. One Mut. No Mut. NGS CFTR Panel (MVCC ) Normal Positive The Future in CF Diagnosis and Treatment: NBS with more CFTR mutations; better education; better communications; miraculous CFTR modulator therapies 6

7 NGS NGS in NBS Technology aspect Capacity and flexibility o WGS o WES o Targeted diseases/genes o Targeted analysis Data storage and management Data interpretation Data reporting Ethical and autonomy issues (genomic technology) WGS/WES NGS in NBS Program aspect First tier testing for some conditions Multiplexing o Multiple diseases o Multiple genes Turnaround time Carrier detection Unknown clinical consequence mutations Cost o NBS testing vs. NBS system Summary Clinical utility Establish capability to screen for new disorders Improve screening performance Technical feasibility Applicable to DBS Turnaround time High throughput Mutation databases and references Method selection Cost concideration Assay validation Qualitative assay vs. quantitative assay Accuracy, precision, reproducibility, linearity, population normal range, clinical validity QA and QC consideration Results interpreting and reporting 7

8 Funding Support The Legacy of Angels Foundation Co founders: Paul and Sue Rosenau Acknowledgments CF IRT/NGS Laboratory Testing Sean Mochal, BS (WSLH) John Moon, MS (WSLH) Michael Cogley, BS (WSLH) Sam Dawe, PhD (WSLH) Anne Atkins, MPH Rachel Morgan, BS CF IRT/NGS Investigators Philip Farrell, MD, PhD (UWSMPH) Michael Rock, MD (UWSMPH) Peggy Modaff, CGC (UWSMPH) Anita Laxova, BS (UWSMPH) 8